Computational and laboratory projects, grouped by subject area. Research placements, my MRes thesis work and industry work live on the Research Portfolio page.
Project · 2023
Annotating an unknown 460-residue protein from sequence alone, from transmembrane topology through profile searches and domain databases to a predicted structure, arriving at a bacterial two-component sensor histidine kinase.
Project · 2022
How a protein with three copies of one domain, no beta sheet at all, and a strongly negative surface manages to carry fatty acids, metals, hormones and much of the drug pharmacopoeia.
Project · 2022
A YASARA practical running from why left-handed helices are rare to manually docking trimethoprim and pyrimethamine into the dihydrofolate reductase active site and counting their contacts.
Project · 2022
Modelling a protein with no experimental structure three different ways, comparing the models against each other and AlphaFold2, and judging which to trust on stereochemistry rather than appearance.
Project · 2022
How a 3 Angstrom filter rejects an ion smaller than the one it passes, while still conducting at roughly 10^8 ions per second.
Project · 2023
Deriving a saturating model of gene expression analytically and numerically, and reading the dynamics of a three-variable linear system out of its eigenvalues.
Project · 2023
Fitting and averaging competing regression models by AIC, then showing with WAIC how badly a model does when it ignores the grouping structure of its own data.
Project · 2023
Two sequence-processing tools written in core Python only, with BioPython and PyCogent banned: a paired-end quality filter and an IUPAC motif searcher that reads both strands.
Project · 2023
A Python program that builds a library of 100 synthetic promoter sequences with defined core-promoter motifs and randomised transcription factor binding sites, ready for Golden Gate assembly.
Project · 2022
A 51-page reproducible R Markdown analysis: visualising a cell-tracking dataset, testing it properly, and working through a full RNA-seq pipeline from raw reads to gene ontology.
Project · 2022
Command-line and R exercises on real files: parsing VCF and SAM, fixing malformed CSV with awk, and pulling live COVID-19 case data from an API.
Project · 2022
Pairwise alignment, a DESeq2 differential expression analysis of a HOXA1 knockdown, and structured queries across Ensembl and COSMIC.
Project · 2023
Identifying a 13.8 kbp unknown fungal sequence, showing that its closest BLAST match was an artefact of unmasked repeats, and combining two gene predictors with BLASTx evidence into a putative gene model.
Project · 2022
A lab report in which the cloning did not work, and the useful part was establishing which step failed: the ligation, not the transformation.
Project · 2022
Designing a vector to express human frataxin with a C-terminal GFP fusion: primers, an enzyme pair that does not cut the gene, and a construct verified in frame at both junctions.